Data explorations
First thing we did was read in the main data file and merge it with the day 0 data. Because the day zero are true for all temperatures, we duplicate the data for the 19 and 55 degree conditions. Then, we convert log-scale the the indicator bacteria counts, adding a dummy value of 1 to prevent errors of logging 0.
main_data <- read.csv("./data/clean/trial_data.csv")
day0 <- read.csv("./data/clean/day0.csv", skip=3, skipNul = T, stringsAsFactors = F)
day0 <- day0 %>% select(-fs_conc, -fs_vol, -inoc_conc, -inoc_vol) %>% spread(key = measurement, value = Value)
day0<- rbind(
day0,
day0 %>% transform(Temp=replace(Temp,Temp==37, 19)),
day0 %>% transform(Temp=replace(Temp,Temp==37, 55))
)
names(main_data)
## [1] "Temp" "OL" "Time" "Recipe" "Ammonia"
## [6] "pH" "sCOD" "TS" "VS" "Coliforms"
## [11] "Ecoli" "Enterococci" "Methane"
names(day0)
## [1] "Recipe" "Temp" "OL" "Time" "Ammonia"
## [6] "Coliforms" "Ecoli" "Enterococci" "Methane" "pH"
## [11] "sCOD" "TS" "VS"
sn_raw <- rbind(main_data, day0)
sn <- sn_raw %>%
rowwise() %>%
transform(
Recipe=as.factor(Recipe),
Ecoli = log10(Ecoli + 1),
Coliforms = log10(Coliforms + 1),
Enterococci = log10(Enterococci + 1))
summary(sn)
## Temp OL Time Recipe Ammonia
## Min. :19 Min. :0.5 Min. :0.000 FWS12:69 Min. : 865
## 1st Qu.:19 1st Qu.:0.5 1st Qu.:3.000 FWS13:69 1st Qu.:1452
## Median :37 Median :2.0 Median :6.000 FWS31:69 Median :1625
## Mean :37 Mean :2.0 Mean :5.217 Mean :1619
## 3rd Qu.:55 3rd Qu.:3.5 3rd Qu.:6.000 3rd Qu.:1768
## Max. :55 Max. :3.5 Max. :9.000 Max. :2305
## pH sCOD TS VS
## Min. :6.840 Min. : 6522 Min. :4.840 Min. :3.120
## 1st Qu.:7.240 1st Qu.: 8262 1st Qu.:5.570 1st Qu.:3.410
## Median :7.440 Median :10111 Median :5.740 Median :3.560
## Mean :7.436 Mean :10502 Mean :5.874 Mean :3.705
## 3rd Qu.:7.510 3rd Qu.:12261 3rd Qu.:6.035 3rd Qu.:3.860
## Max. :8.060 Max. :22965 Max. :8.095 Max. :5.371
## Coliforms Ecoli Enterococci Methane
## Min. :0.000 Min. :0.000 Min. :0.000 Min. : 0.00
## 1st Qu.:2.249 1st Qu.:2.154 1st Qu.:4.511 1st Qu.: 5.75
## Median :4.772 Median :4.502 Median :5.178 Median : 19.50
## Mean :3.857 Mean :3.675 Mean :4.757 Mean : 40.89
## 3rd Qu.:5.380 3rd Qu.:5.255 3rd Qu.:5.871 3rd Qu.: 75.55
## Max. :8.020 Max. :8.020 Max. :7.322 Max. :188.30
It may prove useful to note the components of the three recipes. The organic loading rates were calcualted based on the volitile solid quantity. the recepies are ratios of 2 of three ingrrerdiates (not including the innoculum, which is added as discussed above): dairy cattle slurry(DCS), Fats Oils and Grease (FOG), and restauraant food waste (RFW).
- FWS12: 1:2 FOG:DCS
- FWS13: DCS:RFW 1:3
- FWS31: DCS:RFW 3:1
We add those proportion to the data. Then, we save the cleaned, prepated data.
recipes <- data.frame(
Recipe= c("FWS12","FWS13","FWS31"),
RFW= as.factor(round(c(0, 3/4, 1/4), 2)),
DCS=as.factor(round(c(1/3, 1/4, 3/4),2)),
FOG=as.factor(round(c(2/3, 0, 0), 2))
)
sn <- merge(sn, recipes, by="Recipe")
write.csv(sn, "data/clean/cleaned_combined_minitrial_data.csv")
Note that the conditions were set to have 3 different loading rates, which we will treat as categorical because while they are numerical values of .5, 2, or 3.5, these are not observed values. There for we set them to be factors (which allows for categories to be ranked by a inheirent value).
Next, we can do some explortatory analysis:
sn$OL <- as.factor(sn$OL)
ggscatmat(sn, color="Recipe", alpha = .3) + theme(legend.position = "bottom")
## Warning in ggscatmat(sn, color = "Recipe", alpha = 0.3): Factor variables
## are omitted in plot
#ggpairs(sn, aes(color=Recipe, alpha=.5))
Initial observations:
- the original Box Behnken design can be seen looking at the top left area, seeing the distribution of values between Time, OL, and Temp.
- E. coli and Coliforms are, unsurprisingly, very highly correlated.
- TS and VS are highly correlated
Lets replot without some of the highly correlated ones that
ggscatmat(sn %>% select(-TS, -Coliforms), color="Recipe", alpha = .3) + theme(legend.position = "bottom")
## Warning in ggscatmat(sn %>% select(-TS, -Coliforms), color = "Recipe",
## alpha = 0.3): Factor variables are omitted in plot
Lets look at the indicators
Enterococci
It looks like there is a big effect of temperature: Enterococci die-off only occurs at 55, and there may be a small degree of die-off at 37 for FWS12. Keeping inmind that 55 degree operation is rarely cost effective, lets look without the 55 degree condition.
It appears that nothing dirastic is happening to the Enterococci regardless of recipe for 19 and 37 degrees.
We can further split this out by the proportion of the different componenets in the feedstock
ggplot(sn, aes(x=Time, y=Enterococci, color=as.factor(DCS))) +
geom_point() +
labs(caption=fn("Effect of OL vs DCS"),
subtitle="No effect due to proportion of DCS", color="") +
facet_wrap(~OL+Temp) +
geom_smooth(method = lm)
ggplot(sn, aes(x=Temp, y=Enterococci, color=as.factor(RFW))) +
labs(caption=fn("Effect of Temp"), color="RFW") +
geom_point() + geom_smooth(method = lm)
ggplot(sn, aes(x=Time, y=Enterococci, color=as.factor(Temp))) +
geom_point() +
labs(subtitle="At 19 and 37, presence of RFW increases Enterococci survival",
caption=fn("Effect of RFW"), color="") +
facet_wrap(~RFW) + geom_smooth(method = lm)
Those rates seem to indicate 2 things:
- that the higher proportion of restaurant food waste, the better enterococci survive
- regardless of the proportion of RFW, increased temperature inhibits Enterococci
E. coli
ggplot(sn, aes(x=Time, y=Ecoli, color=as.factor(Temp))) +
geom_point() + geom_smooth(method = lm) +
labs(caption=fn("Effect of Temperature"), color="")
ggplot(sn, aes(x=Time, y=Ecoli, color=as.factor(Temp))) +
geom_point() +
facet_wrap(~OL+Recipe) +
geom_smooth(method = lm) +
labs(caption=fn("Effect of OL and Recipe"), color="")
E coli counts seem to depend largely on Temp rather than OL or Recipe.
This may indicate that while die-off occurs at cold temperature, higher temperatue increases the die-off rate.
While dieoff occurs at 37 and 55, it also appears to occur at 19 with FWS13.
In All cases at low temperatures, lower OL yields better dieoff.
Modelling
stan_data = list(
nbugs=3,
nrows=nrow(sn),
Temp=(sn$Temp -19)/18 + 1,
Ammonia=sn$Ammonia,
pH=sn$pH,
Ecoli=sn$Ecoli,
Coliforms=sn$Coliforms,
Time=sn$Time,
OL=ifelse(sn$OL==.5, 1, ifelse(sn$OL==3.5, 3, sn$OL)),
Enterococci=sn$Enterococci,
sCOD=sn$sCOD,
VS=sn$VS,
TS=sn$TS,
Recipe=as.numeric(sn$Recipe),
Methane=sn$Methane
)
fit <- stan(
file = "./models/model_min.stan",
verbose = T,
chains=4,
data = stan_data
)
##
## TRANSLATING MODEL 'model_min' FROM Stan CODE TO C++ CODE NOW.
## successful in parsing the Stan model 'model_min'.
## recompiling to avoid crashing R session
## OS: x86_64, darwin15.6.0; rstan: 2.18.2; Rcpp: 1.0.1; inline: 0.3.15
## >> setting environment variables:
## PKG_LIBS = -L'/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/lib/' -lStanHeaders
## PKG_CPPFLAGS = -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include/" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/unsupported" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS
## >> Program source :
##
## 1 :
## 2 : // includes from the plugin
## 3 : // [[Rcpp::plugins(cpp14)]]
## 4 :
## 5 : // user includes
## 6 : #define STAN__SERVICES__COMMAND_HPP// Code generated by Stan version 2.18.0
## 7 :
## 8 : #include <stan/model/model_header.hpp>
## 9 :
## 10 : namespace modeld8e35e346352_model_min_namespace {
## 11 :
## 12 : using std::istream;
## 13 : using std::string;
## 14 : using std::stringstream;
## 15 : using std::vector;
## 16 : using stan::io::dump;
## 17 : using stan::math::lgamma;
## 18 : using stan::model::prob_grad;
## 19 : using namespace stan::math;
## 20 :
## 21 : static int current_statement_begin__;
## 22 :
## 23 : stan::io::program_reader prog_reader__() {
## 24 : stan::io::program_reader reader;
## 25 : reader.add_event(0, 0, "start", "modeld8e35e346352_model_min");
## 26 : reader.add_event(59, 57, "end", "modeld8e35e346352_model_min");
## 27 : return reader;
## 28 : }
## 29 :
## 30 : class modeld8e35e346352_model_min : public prob_grad {
## 31 : private:
## 32 : int nrows;
## 33 : int nbugs;
## 34 : vector<double> Ecoli;
## 35 : vector<double> Enterococci;
## 36 : vector<int> Recipe;
## 37 : vector<int> Time;
## 38 : vector<double> sCOD;
## 39 : vector<int> OL;
## 40 : vector<double> VS;
## 41 : vector<double> Ammonia;
## 42 : vector<int> Temp;
## 43 : vector<double> Methane;
## 44 : public:
## 45 : modeld8e35e346352_model_min(stan::io::var_context& context__,
## 46 : std::ostream* pstream__ = 0)
## 47 : : prob_grad(0) {
## 48 : ctor_body(context__, 0, pstream__);
## 49 : }
## 50 :
## 51 : modeld8e35e346352_model_min(stan::io::var_context& context__,
## 52 : unsigned int random_seed__,
## 53 : std::ostream* pstream__ = 0)
## 54 : : prob_grad(0) {
## 55 : ctor_body(context__, random_seed__, pstream__);
## 56 : }
## 57 :
## 58 : void ctor_body(stan::io::var_context& context__,
## 59 : unsigned int random_seed__,
## 60 : std::ostream* pstream__) {
## 61 : typedef double local_scalar_t__;
## 62 :
## 63 : boost::ecuyer1988 base_rng__ =
## 64 : stan::services::util::create_rng(random_seed__, 0);
## 65 : (void) base_rng__; // suppress unused var warning
## 66 :
## 67 : current_statement_begin__ = -1;
## 68 :
## 69 : static const char* function__ = "modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min";
## 70 : (void) function__; // dummy to suppress unused var warning
## 71 : size_t pos__;
## 72 : (void) pos__; // dummy to suppress unused var warning
## 73 : std::vector<int> vals_i__;
## 74 : std::vector<double> vals_r__;
## 75 : local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
## 76 : (void) DUMMY_VAR__; // suppress unused var warning
## 77 :
## 78 : // initialize member variables
## 79 : try {
## 80 : current_statement_begin__ = 2;
## 81 : context__.validate_dims("data initialization", "nrows", "int", context__.to_vec());
## 82 : nrows = int(0);
## 83 : vals_i__ = context__.vals_i("nrows");
## 84 : pos__ = 0;
## 85 : nrows = vals_i__[pos__++];
## 86 : current_statement_begin__ = 3;
## 87 : context__.validate_dims("data initialization", "nbugs", "int", context__.to_vec());
## 88 : nbugs = int(0);
## 89 : vals_i__ = context__.vals_i("nbugs");
## 90 : pos__ = 0;
## 91 : nbugs = vals_i__[pos__++];
## 92 : current_statement_begin__ = 4;
## 93 : validate_non_negative_index("Ecoli", "nrows", nrows);
## 94 : context__.validate_dims("data initialization", "Ecoli", "double", context__.to_vec(nrows));
## 95 : validate_non_negative_index("Ecoli", "nrows", nrows);
## 96 : Ecoli = std::vector<double>(nrows,double(0));
## 97 : vals_r__ = context__.vals_r("Ecoli");
## 98 : pos__ = 0;
## 99 : size_t Ecoli_limit_0__ = nrows;
## 100 : for (size_t i_0__ = 0; i_0__ < Ecoli_limit_0__; ++i_0__) {
## 101 : Ecoli[i_0__] = vals_r__[pos__++];
## 102 : }
## 103 : current_statement_begin__ = 5;
## 104 : validate_non_negative_index("Enterococci", "nrows", nrows);
## 105 : context__.validate_dims("data initialization", "Enterococci", "double", context__.to_vec(nrows));
## 106 : validate_non_negative_index("Enterococci", "nrows", nrows);
## 107 : Enterococci = std::vector<double>(nrows,double(0));
## 108 : vals_r__ = context__.vals_r("Enterococci");
## 109 : pos__ = 0;
## 110 : size_t Enterococci_limit_0__ = nrows;
## 111 : for (size_t i_0__ = 0; i_0__ < Enterococci_limit_0__; ++i_0__) {
## 112 : Enterococci[i_0__] = vals_r__[pos__++];
## 113 : }
## 114 : current_statement_begin__ = 6;
## 115 : validate_non_negative_index("Recipe", "nrows", nrows);
## 116 : context__.validate_dims("data initialization", "Recipe", "int", context__.to_vec(nrows));
## 117 : validate_non_negative_index("Recipe", "nrows", nrows);
## 118 : Recipe = std::vector<int>(nrows,int(0));
## 119 : vals_i__ = context__.vals_i("Recipe");
## 120 : pos__ = 0;
## 121 : size_t Recipe_limit_0__ = nrows;
## 122 : for (size_t i_0__ = 0; i_0__ < Recipe_limit_0__; ++i_0__) {
## 123 : Recipe[i_0__] = vals_i__[pos__++];
## 124 : }
## 125 : current_statement_begin__ = 7;
## 126 : validate_non_negative_index("Time", "nrows", nrows);
## 127 : context__.validate_dims("data initialization", "Time", "int", context__.to_vec(nrows));
## 128 : validate_non_negative_index("Time", "nrows", nrows);
## 129 : Time = std::vector<int>(nrows,int(0));
## 130 : vals_i__ = context__.vals_i("Time");
## 131 : pos__ = 0;
## 132 : size_t Time_limit_0__ = nrows;
## 133 : for (size_t i_0__ = 0; i_0__ < Time_limit_0__; ++i_0__) {
## 134 : Time[i_0__] = vals_i__[pos__++];
## 135 : }
## 136 : current_statement_begin__ = 8;
## 137 : validate_non_negative_index("sCOD", "nrows", nrows);
## 138 : context__.validate_dims("data initialization", "sCOD", "double", context__.to_vec(nrows));
## 139 : validate_non_negative_index("sCOD", "nrows", nrows);
## 140 : sCOD = std::vector<double>(nrows,double(0));
## 141 : vals_r__ = context__.vals_r("sCOD");
## 142 : pos__ = 0;
## 143 : size_t sCOD_limit_0__ = nrows;
## 144 : for (size_t i_0__ = 0; i_0__ < sCOD_limit_0__; ++i_0__) {
## 145 : sCOD[i_0__] = vals_r__[pos__++];
## 146 : }
## 147 : current_statement_begin__ = 9;
## 148 : validate_non_negative_index("OL", "nrows", nrows);
## 149 : context__.validate_dims("data initialization", "OL", "int", context__.to_vec(nrows));
## 150 : validate_non_negative_index("OL", "nrows", nrows);
## 151 : OL = std::vector<int>(nrows,int(0));
## 152 : vals_i__ = context__.vals_i("OL");
## 153 : pos__ = 0;
## 154 : size_t OL_limit_0__ = nrows;
## 155 : for (size_t i_0__ = 0; i_0__ < OL_limit_0__; ++i_0__) {
## 156 : OL[i_0__] = vals_i__[pos__++];
## 157 : }
## 158 : current_statement_begin__ = 10;
## 159 : validate_non_negative_index("VS", "nrows", nrows);
## 160 : context__.validate_dims("data initialization", "VS", "double", context__.to_vec(nrows));
## 161 : validate_non_negative_index("VS", "nrows", nrows);
## 162 : VS = std::vector<double>(nrows,double(0));
## 163 : vals_r__ = context__.vals_r("VS");
## 164 : pos__ = 0;
## 165 : size_t VS_limit_0__ = nrows;
## 166 : for (size_t i_0__ = 0; i_0__ < VS_limit_0__; ++i_0__) {
## 167 : VS[i_0__] = vals_r__[pos__++];
## 168 : }
## 169 : current_statement_begin__ = 11;
## 170 : validate_non_negative_index("Ammonia", "nrows", nrows);
## 171 : context__.validate_dims("data initialization", "Ammonia", "double", context__.to_vec(nrows));
## 172 : validate_non_negative_index("Ammonia", "nrows", nrows);
## 173 : Ammonia = std::vector<double>(nrows,double(0));
## 174 : vals_r__ = context__.vals_r("Ammonia");
## 175 : pos__ = 0;
## 176 : size_t Ammonia_limit_0__ = nrows;
## 177 : for (size_t i_0__ = 0; i_0__ < Ammonia_limit_0__; ++i_0__) {
## 178 : Ammonia[i_0__] = vals_r__[pos__++];
## 179 : }
## 180 : current_statement_begin__ = 12;
## 181 : validate_non_negative_index("Temp", "nrows", nrows);
## 182 : context__.validate_dims("data initialization", "Temp", "int", context__.to_vec(nrows));
## 183 : validate_non_negative_index("Temp", "nrows", nrows);
## 184 : Temp = std::vector<int>(nrows,int(0));
## 185 : vals_i__ = context__.vals_i("Temp");
## 186 : pos__ = 0;
## 187 : size_t Temp_limit_0__ = nrows;
## 188 : for (size_t i_0__ = 0; i_0__ < Temp_limit_0__; ++i_0__) {
## 189 : Temp[i_0__] = vals_i__[pos__++];
## 190 : }
## 191 : current_statement_begin__ = 13;
## 192 : validate_non_negative_index("Methane", "nrows", nrows);
## 193 : context__.validate_dims("data initialization", "Methane", "double", context__.to_vec(nrows));
## 194 : validate_non_negative_index("Methane", "nrows", nrows);
## 195 : Methane = std::vector<double>(nrows,double(0));
## 196 : vals_r__ = context__.vals_r("Methane");
## 197 : pos__ = 0;
## 198 : size_t Methane_limit_0__ = nrows;
## 199 : for (size_t i_0__ = 0; i_0__ < Methane_limit_0__; ++i_0__) {
## 200 : Methane[i_0__] = vals_r__[pos__++];
## 201 : }
## 202 :
## 203 : // validate, data variables
## 204 : current_statement_begin__ = 2;
## 205 : check_greater_or_equal(function__,"nrows",nrows,0);
## 206 : current_statement_begin__ = 3;
## 207 : check_greater_or_equal(function__,"nbugs",nbugs,0);
## 208 : current_statement_begin__ = 4;
## 209 : current_statement_begin__ = 5;
## 210 : current_statement_begin__ = 6;
## 211 : current_statement_begin__ = 7;
## 212 : current_statement_begin__ = 8;
## 213 : current_statement_begin__ = 9;
## 214 : current_statement_begin__ = 10;
## 215 : current_statement_begin__ = 11;
## 216 : current_statement_begin__ = 12;
## 217 : current_statement_begin__ = 13;
## 218 : // initialize data variables
## 219 :
## 220 :
## 221 : // validate transformed data
## 222 :
## 223 : // validate, set parameter ranges
## 224 : num_params_r__ = 0U;
## 225 : param_ranges_i__.clear();
## 226 : current_statement_begin__ = 16;
## 227 : validate_non_negative_index("recipe_effect_m", "3", 3);
## 228 : num_params_r__ += 3;
## 229 : current_statement_begin__ = 17;
## 230 : validate_non_negative_index("temp_effect_m", "3", 3);
## 231 : num_params_r__ += 3;
## 232 : current_statement_begin__ = 18;
## 233 : validate_non_negative_index("ol_effect_m", "3", 3);
## 234 : num_params_r__ += 3;
## 235 : current_statement_begin__ = 19;
## 236 : validate_non_negative_index("recipe_effect_b", "3", 3);
## 237 : num_params_r__ += 3;
## 238 : current_statement_begin__ = 20;
## 239 : validate_non_negative_index("temp_effect_b", "3", 3);
## 240 : num_params_r__ += 3;
## 241 : current_statement_begin__ = 21;
## 242 : validate_non_negative_index("ol_effect_b", "3", 3);
## 243 : num_params_r__ += 3;
## 244 : current_statement_begin__ = 22;
## 245 : ++num_params_r__;
## 246 : current_statement_begin__ = 23;
## 247 : ++num_params_r__;
## 248 : } catch (const std::exception& e) {
## 249 : stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
## 250 : // Next line prevents compiler griping about no return
## 251 : throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
## 252 : }
## 253 : }
## 254 :
## 255 : ~modeld8e35e346352_model_min() { }
## 256 :
## 257 :
## 258 : void transform_inits(const stan::io::var_context& context__,
## 259 : std::vector<int>& params_i__,
## 260 : std::vector<double>& params_r__,
## 261 : std::ostream* pstream__) const {
## 262 : stan::io::writer<double> writer__(params_r__,params_i__);
## 263 : size_t pos__;
## 264 : (void) pos__; // dummy call to supress warning
## 265 : std::vector<double> vals_r__;
## 266 : std::vector<int> vals_i__;
## 267 :
## 268 : if (!(context__.contains_r("recipe_effect_m")))
## 269 : throw std::runtime_error("variable recipe_effect_m missing");
## 270 : vals_r__ = context__.vals_r("recipe_effect_m");
## 271 : pos__ = 0U;
## 272 : validate_non_negative_index("recipe_effect_m", "3", 3);
## 273 : context__.validate_dims("initialization", "recipe_effect_m", "double", context__.to_vec(3));
## 274 : std::vector<double> recipe_effect_m(3,double(0));
## 275 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 276 : recipe_effect_m[i0__] = vals_r__[pos__++];
## 277 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 278 : try {
## 279 : writer__.scalar_unconstrain(recipe_effect_m[i0__]);
## 280 : } catch (const std::exception& e) {
## 281 : throw std::runtime_error(std::string("Error transforming variable recipe_effect_m: ") + e.what());
## 282 : }
## 283 :
## 284 : if (!(context__.contains_r("temp_effect_m")))
## 285 : throw std::runtime_error("variable temp_effect_m missing");
## 286 : vals_r__ = context__.vals_r("temp_effect_m");
## 287 : pos__ = 0U;
## 288 : validate_non_negative_index("temp_effect_m", "3", 3);
## 289 : context__.validate_dims("initialization", "temp_effect_m", "double", context__.to_vec(3));
## 290 : std::vector<double> temp_effect_m(3,double(0));
## 291 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 292 : temp_effect_m[i0__] = vals_r__[pos__++];
## 293 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 294 : try {
## 295 : writer__.scalar_unconstrain(temp_effect_m[i0__]);
## 296 : } catch (const std::exception& e) {
## 297 : throw std::runtime_error(std::string("Error transforming variable temp_effect_m: ") + e.what());
## 298 : }
## 299 :
## 300 : if (!(context__.contains_r("ol_effect_m")))
## 301 : throw std::runtime_error("variable ol_effect_m missing");
## 302 : vals_r__ = context__.vals_r("ol_effect_m");
## 303 : pos__ = 0U;
## 304 : validate_non_negative_index("ol_effect_m", "3", 3);
## 305 : context__.validate_dims("initialization", "ol_effect_m", "double", context__.to_vec(3));
## 306 : std::vector<double> ol_effect_m(3,double(0));
## 307 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 308 : ol_effect_m[i0__] = vals_r__[pos__++];
## 309 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 310 : try {
## 311 : writer__.scalar_unconstrain(ol_effect_m[i0__]);
## 312 : } catch (const std::exception& e) {
## 313 : throw std::runtime_error(std::string("Error transforming variable ol_effect_m: ") + e.what());
## 314 : }
## 315 :
## 316 : if (!(context__.contains_r("recipe_effect_b")))
## 317 : throw std::runtime_error("variable recipe_effect_b missing");
## 318 : vals_r__ = context__.vals_r("recipe_effect_b");
## 319 : pos__ = 0U;
## 320 : validate_non_negative_index("recipe_effect_b", "3", 3);
## 321 : context__.validate_dims("initialization", "recipe_effect_b", "double", context__.to_vec(3));
## 322 : std::vector<double> recipe_effect_b(3,double(0));
## 323 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 324 : recipe_effect_b[i0__] = vals_r__[pos__++];
## 325 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 326 : try {
## 327 : writer__.scalar_unconstrain(recipe_effect_b[i0__]);
## 328 : } catch (const std::exception& e) {
## 329 : throw std::runtime_error(std::string("Error transforming variable recipe_effect_b: ") + e.what());
## 330 : }
## 331 :
## 332 : if (!(context__.contains_r("temp_effect_b")))
## 333 : throw std::runtime_error("variable temp_effect_b missing");
## 334 : vals_r__ = context__.vals_r("temp_effect_b");
## 335 : pos__ = 0U;
## 336 : validate_non_negative_index("temp_effect_b", "3", 3);
## 337 : context__.validate_dims("initialization", "temp_effect_b", "double", context__.to_vec(3));
## 338 : std::vector<double> temp_effect_b(3,double(0));
## 339 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 340 : temp_effect_b[i0__] = vals_r__[pos__++];
## 341 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 342 : try {
## 343 : writer__.scalar_unconstrain(temp_effect_b[i0__]);
## 344 : } catch (const std::exception& e) {
## 345 : throw std::runtime_error(std::string("Error transforming variable temp_effect_b: ") + e.what());
## 346 : }
## 347 :
## 348 : if (!(context__.contains_r("ol_effect_b")))
## 349 : throw std::runtime_error("variable ol_effect_b missing");
## 350 : vals_r__ = context__.vals_r("ol_effect_b");
## 351 : pos__ = 0U;
## 352 : validate_non_negative_index("ol_effect_b", "3", 3);
## 353 : context__.validate_dims("initialization", "ol_effect_b", "double", context__.to_vec(3));
## 354 : std::vector<double> ol_effect_b(3,double(0));
## 355 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 356 : ol_effect_b[i0__] = vals_r__[pos__++];
## 357 : for (int i0__ = 0U; i0__ < 3; ++i0__)
## 358 : try {
## 359 : writer__.scalar_unconstrain(ol_effect_b[i0__]);
## 360 : } catch (const std::exception& e) {
## 361 : throw std::runtime_error(std::string("Error transforming variable ol_effect_b: ") + e.what());
## 362 : }
## 363 :
## 364 : if (!(context__.contains_r("sigma")))
## 365 : throw std::runtime_error("variable sigma missing");
## 366 : vals_r__ = context__.vals_r("sigma");
## 367 : pos__ = 0U;
## 368 : context__.validate_dims("initialization", "sigma", "double", context__.to_vec());
## 369 : double sigma(0);
## 370 : sigma = vals_r__[pos__++];
## 371 : try {
## 372 : writer__.scalar_lb_unconstrain(0,sigma);
## 373 : } catch (const std::exception& e) {
## 374 : throw std::runtime_error(std::string("Error transforming variable sigma: ") + e.what());
## 375 : }
## 376 :
## 377 : if (!(context__.contains_r("sigma_b")))
## 378 : throw std::runtime_error("variable sigma_b missing");
## 379 : vals_r__ = context__.vals_r("sigma_b");
## 380 : pos__ = 0U;
## 381 : context__.validate_dims("initialization", "sigma_b", "double", context__.to_vec());
## 382 : double sigma_b(0);
## 383 : sigma_b = vals_r__[pos__++];
## 384 : try {
## 385 : writer__.scalar_lb_unconstrain(0,sigma_b);
## 386 : } catch (const std::exception& e) {
## 387 : throw std::runtime_error(std::string("Error transforming variable sigma_b: ") + e.what());
## 388 : }
## 389 :
## 390 : params_r__ = writer__.data_r();
## 391 : params_i__ = writer__.data_i();
## 392 : }
## 393 :
## 394 : void transform_inits(const stan::io::var_context& context,
## 395 : Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
## 396 : std::ostream* pstream__) const {
## 397 : std::vector<double> params_r_vec;
## 398 : std::vector<int> params_i_vec;
## 399 : transform_inits(context, params_i_vec, params_r_vec, pstream__);
## 400 : params_r.resize(params_r_vec.size());
## 401 : for (int i = 0; i < params_r.size(); ++i)
## 402 : params_r(i) = params_r_vec[i];
## 403 : }
## 404 :
## 405 :
## 406 : template <bool propto__, bool jacobian__, typename T__>
## 407 : T__ log_prob(vector<T__>& params_r__,
## 408 : vector<int>& params_i__,
## 409 : std::ostream* pstream__ = 0) const {
## 410 :
## 411 : typedef T__ local_scalar_t__;
## 412 :
## 413 : local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
## 414 : (void) DUMMY_VAR__; // suppress unused var warning
## 415 :
## 416 : T__ lp__(0.0);
## 417 : stan::math::accumulator<T__> lp_accum__;
## 418 :
## 419 : try {
## 420 : // model parameters
## 421 : stan::io::reader<local_scalar_t__> in__(params_r__,params_i__);
## 422 :
## 423 : vector<local_scalar_t__> recipe_effect_m;
## 424 : size_t dim_recipe_effect_m_0__ = 3;
## 425 : recipe_effect_m.reserve(dim_recipe_effect_m_0__);
## 426 : for (size_t k_0__ = 0; k_0__ < dim_recipe_effect_m_0__; ++k_0__) {
## 427 : if (jacobian__)
## 428 : recipe_effect_m.push_back(in__.scalar_constrain(lp__));
## 429 : else
## 430 : recipe_effect_m.push_back(in__.scalar_constrain());
## 431 : }
## 432 :
## 433 : vector<local_scalar_t__> temp_effect_m;
## 434 : size_t dim_temp_effect_m_0__ = 3;
## 435 : temp_effect_m.reserve(dim_temp_effect_m_0__);
## 436 : for (size_t k_0__ = 0; k_0__ < dim_temp_effect_m_0__; ++k_0__) {
## 437 : if (jacobian__)
## 438 : temp_effect_m.push_back(in__.scalar_constrain(lp__));
## 439 : else
## 440 : temp_effect_m.push_back(in__.scalar_constrain());
## 441 : }
## 442 :
## 443 : vector<local_scalar_t__> ol_effect_m;
## 444 : size_t dim_ol_effect_m_0__ = 3;
## 445 : ol_effect_m.reserve(dim_ol_effect_m_0__);
## 446 : for (size_t k_0__ = 0; k_0__ < dim_ol_effect_m_0__; ++k_0__) {
## 447 : if (jacobian__)
## 448 : ol_effect_m.push_back(in__.scalar_constrain(lp__));
## 449 : else
## 450 : ol_effect_m.push_back(in__.scalar_constrain());
## 451 : }
## 452 :
## 453 : vector<local_scalar_t__> recipe_effect_b;
## 454 : size_t dim_recipe_effect_b_0__ = 3;
## 455 : recipe_effect_b.reserve(dim_recipe_effect_b_0__);
## 456 : for (size_t k_0__ = 0; k_0__ < dim_recipe_effect_b_0__; ++k_0__) {
## 457 : if (jacobian__)
## 458 : recipe_effect_b.push_back(in__.scalar_constrain(lp__));
## 459 : else
## 460 : recipe_effect_b.push_back(in__.scalar_constrain());
## 461 : }
## 462 :
## 463 : vector<local_scalar_t__> temp_effect_b;
## 464 : size_t dim_temp_effect_b_0__ = 3;
## 465 : temp_effect_b.reserve(dim_temp_effect_b_0__);
## 466 : for (size_t k_0__ = 0; k_0__ < dim_temp_effect_b_0__; ++k_0__) {
## 467 : if (jacobian__)
## 468 : temp_effect_b.push_back(in__.scalar_constrain(lp__));
## 469 : else
## 470 : temp_effect_b.push_back(in__.scalar_constrain());
## 471 : }
## 472 :
## 473 : vector<local_scalar_t__> ol_effect_b;
## 474 : size_t dim_ol_effect_b_0__ = 3;
## 475 : ol_effect_b.reserve(dim_ol_effect_b_0__);
## 476 : for (size_t k_0__ = 0; k_0__ < dim_ol_effect_b_0__; ++k_0__) {
## 477 : if (jacobian__)
## 478 : ol_effect_b.push_back(in__.scalar_constrain(lp__));
## 479 : else
## 480 : ol_effect_b.push_back(in__.scalar_constrain());
## 481 : }
## 482 :
## 483 : local_scalar_t__ sigma;
## 484 : (void) sigma; // dummy to suppress unused var warning
## 485 : if (jacobian__)
## 486 : sigma = in__.scalar_lb_constrain(0,lp__);
## 487 : else
## 488 : sigma = in__.scalar_lb_constrain(0);
## 489 :
## 490 : local_scalar_t__ sigma_b;
## 491 : (void) sigma_b; // dummy to suppress unused var warning
## 492 : if (jacobian__)
## 493 : sigma_b = in__.scalar_lb_constrain(0,lp__);
## 494 : else
## 495 : sigma_b = in__.scalar_lb_constrain(0);
## 496 :
## 497 :
## 498 : // transformed parameters
## 499 : current_statement_begin__ = 26;
## 500 : validate_non_negative_index("coli_hat", "nrows", nrows);
## 501 : Eigen::Matrix<local_scalar_t__,Eigen::Dynamic,1> coli_hat(static_cast<Eigen::VectorXd::Index>(nrows));
## 502 : (void) coli_hat; // dummy to suppress unused var warning
## 503 :
## 504 : stan::math::initialize(coli_hat, DUMMY_VAR__);
## 505 : stan::math::fill(coli_hat,DUMMY_VAR__);
## 506 : current_statement_begin__ = 27;
## 507 : validate_non_negative_index("cocci_hat", "nrows", nrows);
## 508 : Eigen::Matrix<local_scalar_t__,Eigen::Dynamic,1> cocci_hat(static_cast<Eigen::VectorXd::Index>(nrows));
## 509 : (void) cocci_hat; // dummy to suppress unused var warning
## 510 :
## 511 : stan::math::initialize(cocci_hat, DUMMY_VAR__);
## 512 : stan::math::fill(cocci_hat,DUMMY_VAR__);
## 513 :
## 514 :
## 515 : current_statement_begin__ = 28;
## 516 : for (int i = 1; i <= nrows; ++i) {
## 517 :
## 518 : current_statement_begin__ = 29;
## 519 : stan::model::assign(coli_hat,
## 520 : stan::model::cons_list(stan::model::index_uni(i), stan::model::nil_index_list()),
## 521 : ((((get_base1(temp_effect_m,get_base1(Temp,i,"Temp",1),"temp_effect_m",1) + get_base1(recipe_effect_m,get_base1(Recipe,i,"Recipe",1),"recipe_effect_m",1)) + get_base1(ol_effect_m,get_base1(OL,i,"OL",1),"ol_effect_m",1)) * get_base1(Time,i,"Time",1)) + ((get_base1(recipe_effect_b,get_base1(Recipe,i,"Recipe",1),"recipe_effect_b",1) + get_base1(temp_effect_b,get_base1(Temp,i,"Temp",1),"temp_effect_b",1)) + get_base1(ol_effect_b,get_base1(OL,i,"OL",1),"ol_effect_b",1))),
## 522 : "assigning variable coli_hat");
## 523 : current_statement_begin__ = 30;
## 524 : stan::model::assign(cocci_hat,
## 525 : stan::model::cons_list(stan::model::index_uni(i), stan::model::nil_index_list()),
## 526 : ((((get_base1(temp_effect_m,get_base1(Temp,i,"Temp",1),"temp_effect_m",1) + get_base1(recipe_effect_m,get_base1(Recipe,i,"Recipe",1),"recipe_effect_m",1)) + get_base1(ol_effect_m,get_base1(OL,i,"OL",1),"ol_effect_m",1)) * get_base1(Time,i,"Time",1)) + ((get_base1(recipe_effect_b,get_base1(Recipe,i,"Recipe",1),"recipe_effect_b",1) + get_base1(temp_effect_b,get_base1(Temp,i,"Temp",1),"temp_effect_b",1)) + get_base1(ol_effect_b,get_base1(OL,i,"OL",1),"ol_effect_b",1))),
## 527 : "assigning variable cocci_hat");
## 528 : }
## 529 :
## 530 : // validate transformed parameters
## 531 : for (int i0__ = 0; i0__ < nrows; ++i0__) {
## 532 : if (stan::math::is_uninitialized(coli_hat(i0__))) {
## 533 : std::stringstream msg__;
## 534 : msg__ << "Undefined transformed parameter: coli_hat" << '[' << i0__ << ']';
## 535 : throw std::runtime_error(msg__.str());
## 536 : }
## 537 : }
## 538 : for (int i0__ = 0; i0__ < nrows; ++i0__) {
## 539 : if (stan::math::is_uninitialized(cocci_hat(i0__))) {
## 540 : std::stringstream msg__;
## 541 : msg__ << "Undefined transformed parameter: cocci_hat" << '[' << i0__ << ']';
## 542 : throw std::runtime_error(msg__.str());
## 543 : }
## 544 : }
## 545 :
## 546 : const char* function__ = "validate transformed params";
## 547 : (void) function__; // dummy to suppress unused var warning
## 548 : current_statement_begin__ = 26;
## 549 : current_statement_begin__ = 27;
## 550 :
## 551 : // model body
## 552 :
## 553 : current_statement_begin__ = 42;
## 554 : lp_accum__.add(cauchy_log<propto__>(sigma, 0, 1));
## 555 : current_statement_begin__ = 43;
## 556 : lp_accum__.add(cauchy_log<propto__>(sigma_b, 0, 1));
## 557 : current_statement_begin__ = 44;
## 558 : lp_accum__.add(cauchy_log<propto__>(recipe_effect_b, 0, 1));
## 559 : current_statement_begin__ = 45;
## 560 : lp_accum__.add(cauchy_log<propto__>(recipe_effect_m, 0, 1));
## 561 : current_statement_begin__ = 46;
## 562 : lp_accum__.add(cauchy_log<propto__>(ol_effect_m, 0, 1));
## 563 : current_statement_begin__ = 47;
## 564 : lp_accum__.add(cauchy_log<propto__>(ol_effect_b, 0, 1));
## 565 : current_statement_begin__ = 48;
## 566 : lp_accum__.add(cauchy_log<propto__>(temp_effect_m, 0, 1));
## 567 : current_statement_begin__ = 49;
## 568 : lp_accum__.add(cauchy_log<propto__>(temp_effect_b, 0, 1));
## 569 : current_statement_begin__ = 54;
## 570 : lp_accum__.add(normal_log<propto__>(Ecoli, coli_hat, sigma));
## 571 : current_statement_begin__ = 55;
## 572 : lp_accum__.add(normal_log<propto__>(Enterococci, cocci_hat, sigma_b));
## 573 :
## 574 : } catch (const std::exception& e) {
## 575 : stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
## 576 : // Next line prevents compiler griping about no return
## 577 : throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
## 578 : }
## 579 :
## 580 : lp_accum__.add(lp__);
## 581 : return lp_accum__.sum();
## 582 :
## 583 : } // log_prob()
## 584 :
## 585 : template <bool propto, bool jacobian, typename T_>
## 586 : T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
## 587 : std::ostream* pstream = 0) const {
## 588 : std::vector<T_> vec_params_r;
## 589 : vec_params_r.reserve(params_r.size());
## 590 : for (int i = 0; i < params_r.size(); ++i)
## 591 : vec_params_r.push_back(params_r(i));
## 592 : std::vector<int> vec_params_i;
## 593 : return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, pstream);
## 594 : }
## 595 :
## 596 :
## 597 : void get_param_names(std::vector<std::string>& names__) const {
## 598 : names__.resize(0);
## 599 : names__.push_back("recipe_effect_m");
## 600 : names__.push_back("temp_effect_m");
## 601 : names__.push_back("ol_effect_m");
## 602 : names__.push_back("recipe_effect_b");
## 603 : names__.push_back("temp_effect_b");
## 604 : names__.push_back("ol_effect_b");
## 605 : names__.push_back("sigma");
## 606 : names__.push_back("sigma_b");
## 607 : names__.push_back("coli_hat");
## 608 : names__.push_back("cocci_hat");
## 609 : }
## 610 :
## 611 :
## 612 : void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
## 613 : dimss__.resize(0);
## 614 : std::vector<size_t> dims__;
## 615 : dims__.resize(0);
## 616 : dims__.push_back(3);
## 617 : dimss__.push_back(dims__);
## 618 : dims__.resize(0);
## 619 : dims__.push_back(3);
## 620 : dimss__.push_back(dims__);
## 621 : dims__.resize(0);
## 622 : dims__.push_back(3);
## 623 : dimss__.push_back(dims__);
## 624 : dims__.resize(0);
## 625 : dims__.push_back(3);
## 626 : dimss__.push_back(dims__);
## 627 : dims__.resize(0);
## 628 : dims__.push_back(3);
## 629 : dimss__.push_back(dims__);
## 630 : dims__.resize(0);
## 631 : dims__.push_back(3);
## 632 : dimss__.push_back(dims__);
## 633 : dims__.resize(0);
## 634 : dimss__.push_back(dims__);
## 635 : dims__.resize(0);
## 636 : dimss__.push_back(dims__);
## 637 : dims__.resize(0);
## 638 : dims__.push_back(nrows);
## 639 : dimss__.push_back(dims__);
## 640 : dims__.resize(0);
## 641 : dims__.push_back(nrows);
## 642 : dimss__.push_back(dims__);
## 643 : }
## 644 :
## 645 : template <typename RNG>
## 646 : void write_array(RNG& base_rng__,
## 647 : std::vector<double>& params_r__,
## 648 : std::vector<int>& params_i__,
## 649 : std::vector<double>& vars__,
## 650 : bool include_tparams__ = true,
## 651 : bool include_gqs__ = true,
## 652 : std::ostream* pstream__ = 0) const {
## 653 : typedef double local_scalar_t__;
## 654 :
## 655 : vars__.resize(0);
## 656 : stan::io::reader<local_scalar_t__> in__(params_r__,params_i__);
## 657 : static const char* function__ = "modeld8e35e346352_model_min_namespace::write_array";
## 658 : (void) function__; // dummy to suppress unused var warning
## 659 : // read-transform, write parameters
## 660 : vector<double> recipe_effect_m;
## 661 : size_t dim_recipe_effect_m_0__ = 3;
## 662 : for (size_t k_0__ = 0; k_0__ < dim_recipe_effect_m_0__; ++k_0__) {
## 663 : recipe_effect_m.push_back(in__.scalar_constrain());
## 664 : }
## 665 : vector<double> temp_effect_m;
## 666 : size_t dim_temp_effect_m_0__ = 3;
## 667 : for (size_t k_0__ = 0; k_0__ < dim_temp_effect_m_0__; ++k_0__) {
## 668 : temp_effect_m.push_back(in__.scalar_constrain());
## 669 : }
## 670 : vector<double> ol_effect_m;
## 671 : size_t dim_ol_effect_m_0__ = 3;
## 672 : for (size_t k_0__ = 0; k_0__ < dim_ol_effect_m_0__; ++k_0__) {
## 673 : ol_effect_m.push_back(in__.scalar_constrain());
## 674 : }
## 675 : vector<double> recipe_effect_b;
## 676 : size_t dim_recipe_effect_b_0__ = 3;
## 677 : for (size_t k_0__ = 0; k_0__ < dim_recipe_effect_b_0__; ++k_0__) {
## 678 : recipe_effect_b.push_back(in__.scalar_constrain());
## 679 : }
## 680 : vector<double> temp_effect_b;
## 681 : size_t dim_temp_effect_b_0__ = 3;
## 682 : for (size_t k_0__ = 0; k_0__ < dim_temp_effect_b_0__; ++k_0__) {
## 683 : temp_effect_b.push_back(in__.scalar_constrain());
## 684 : }
## 685 : vector<double> ol_effect_b;
## 686 : size_t dim_ol_effect_b_0__ = 3;
## 687 : for (size_t k_0__ = 0; k_0__ < dim_ol_effect_b_0__; ++k_0__) {
## 688 : ol_effect_b.push_back(in__.scalar_constrain());
## 689 : }
## 690 : double sigma = in__.scalar_lb_constrain(0);
## 691 : double sigma_b = in__.scalar_lb_constrain(0);
## 692 : for (int k_0__ = 0; k_0__ < 3; ++k_0__) {
## 693 : vars__.push_back(recipe_effect_m[k_0__]);
## 694 : }
## 695 : for (int k_0__ = 0; k_0__ < 3; ++k_0__) {
## 696 : vars__.push_back(temp_effect_m[k_0__]);
## 697 : }
## 698 : for (int k_0__ = 0; k_0__ < 3; ++k_0__) {
## 699 : vars__.push_back(ol_effect_m[k_0__]);
## 700 : }
## 701 : for (int k_0__ = 0; k_0__ < 3; ++k_0__) {
## 702 : vars__.push_back(recipe_effect_b[k_0__]);
## 703 : }
## 704 : for (int k_0__ = 0; k_0__ < 3; ++k_0__) {
## 705 : vars__.push_back(temp_effect_b[k_0__]);
## 706 : }
## 707 : for (int k_0__ = 0; k_0__ < 3; ++k_0__) {
## 708 : vars__.push_back(ol_effect_b[k_0__]);
## 709 : }
## 710 : vars__.push_back(sigma);
## 711 : vars__.push_back(sigma_b);
## 712 :
## 713 : // declare and define transformed parameters
## 714 : double lp__ = 0.0;
## 715 : (void) lp__; // dummy to suppress unused var warning
## 716 : stan::math::accumulator<double> lp_accum__;
## 717 :
## 718 : local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
## 719 : (void) DUMMY_VAR__; // suppress unused var warning
## 720 :
## 721 : try {
## 722 : current_statement_begin__ = 26;
## 723 : validate_non_negative_index("coli_hat", "nrows", nrows);
## 724 : Eigen::Matrix<local_scalar_t__,Eigen::Dynamic,1> coli_hat(static_cast<Eigen::VectorXd::Index>(nrows));
## 725 : (void) coli_hat; // dummy to suppress unused var warning
## 726 :
## 727 : stan::math::initialize(coli_hat, DUMMY_VAR__);
## 728 : stan::math::fill(coli_hat,DUMMY_VAR__);
## 729 : current_statement_begin__ = 27;
## 730 : validate_non_negative_index("cocci_hat", "nrows", nrows);
## 731 : Eigen::Matrix<local_scalar_t__,Eigen::Dynamic,1> cocci_hat(static_cast<Eigen::VectorXd::Index>(nrows));
## 732 : (void) cocci_hat; // dummy to suppress unused var warning
## 733 :
## 734 : stan::math::initialize(cocci_hat, DUMMY_VAR__);
## 735 : stan::math::fill(cocci_hat,DUMMY_VAR__);
## 736 :
## 737 :
## 738 : current_statement_begin__ = 28;
## 739 : for (int i = 1; i <= nrows; ++i) {
## 740 :
## 741 : current_statement_begin__ = 29;
## 742 : stan::model::assign(coli_hat,
## 743 : stan::model::cons_list(stan::model::index_uni(i), stan::model::nil_index_list()),
## 744 : ((((get_base1(temp_effect_m,get_base1(Temp,i,"Temp",1),"temp_effect_m",1) + get_base1(recipe_effect_m,get_base1(Recipe,i,"Recipe",1),"recipe_effect_m",1)) + get_base1(ol_effect_m,get_base1(OL,i,"OL",1),"ol_effect_m",1)) * get_base1(Time,i,"Time",1)) + ((get_base1(recipe_effect_b,get_base1(Recipe,i,"Recipe",1),"recipe_effect_b",1) + get_base1(temp_effect_b,get_base1(Temp,i,"Temp",1),"temp_effect_b",1)) + get_base1(ol_effect_b,get_base1(OL,i,"OL",1),"ol_effect_b",1))),
## 745 : "assigning variable coli_hat");
## 746 : current_statement_begin__ = 30;
## 747 : stan::model::assign(cocci_hat,
## 748 : stan::model::cons_list(stan::model::index_uni(i), stan::model::nil_index_list()),
## 749 : ((((get_base1(temp_effect_m,get_base1(Temp,i,"Temp",1),"temp_effect_m",1) + get_base1(recipe_effect_m,get_base1(Recipe,i,"Recipe",1),"recipe_effect_m",1)) + get_base1(ol_effect_m,get_base1(OL,i,"OL",1),"ol_effect_m",1)) * get_base1(Time,i,"Time",1)) + ((get_base1(recipe_effect_b,get_base1(Recipe,i,"Recipe",1),"recipe_effect_b",1) + get_base1(temp_effect_b,get_base1(Temp,i,"Temp",1),"temp_effect_b",1)) + get_base1(ol_effect_b,get_base1(OL,i,"OL",1),"ol_effect_b",1))),
## 750 : "assigning variable cocci_hat");
## 751 : }
## 752 :
## 753 : // validate transformed parameters
## 754 : current_statement_begin__ = 26;
## 755 : current_statement_begin__ = 27;
## 756 :
## 757 : // write transformed parameters
## 758 : if (include_tparams__) {
## 759 : for (int k_0__ = 0; k_0__ < nrows; ++k_0__) {
## 760 : vars__.push_back(coli_hat[k_0__]);
## 761 : }
## 762 : for (int k_0__ = 0; k_0__ < nrows; ++k_0__) {
## 763 : vars__.push_back(cocci_hat[k_0__]);
## 764 : }
## 765 : }
## 766 : if (!include_gqs__) return;
## 767 : // declare and define generated quantities
## 768 :
## 769 :
## 770 :
## 771 : // validate generated quantities
## 772 :
## 773 : // write generated quantities
## 774 : } catch (const std::exception& e) {
## 775 : stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
## 776 : // Next line prevents compiler griping about no return
## 777 : throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
## 778 : }
## 779 : }
## 780 :
## 781 : template <typename RNG>
## 782 : void write_array(RNG& base_rng,
## 783 : Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
## 784 : Eigen::Matrix<double,Eigen::Dynamic,1>& vars,
## 785 : bool include_tparams = true,
## 786 : bool include_gqs = true,
## 787 : std::ostream* pstream = 0) const {
## 788 : std::vector<double> params_r_vec(params_r.size());
## 789 : for (int i = 0; i < params_r.size(); ++i)
## 790 : params_r_vec[i] = params_r(i);
## 791 : std::vector<double> vars_vec;
## 792 : std::vector<int> params_i_vec;
## 793 : write_array(base_rng,params_r_vec,params_i_vec,vars_vec,include_tparams,include_gqs,pstream);
## 794 : vars.resize(vars_vec.size());
## 795 : for (int i = 0; i < vars.size(); ++i)
## 796 : vars(i) = vars_vec[i];
## 797 : }
## 798 :
## 799 : static std::string model_name() {
## 800 : return "modeld8e35e346352_model_min";
## 801 : }
## 802 :
## 803 :
## 804 : void constrained_param_names(std::vector<std::string>& param_names__,
## 805 : bool include_tparams__ = true,
## 806 : bool include_gqs__ = true) const {
## 807 : std::stringstream param_name_stream__;
## 808 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 809 : param_name_stream__.str(std::string());
## 810 : param_name_stream__ << "recipe_effect_m" << '.' << k_0__;
## 811 : param_names__.push_back(param_name_stream__.str());
## 812 : }
## 813 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 814 : param_name_stream__.str(std::string());
## 815 : param_name_stream__ << "temp_effect_m" << '.' << k_0__;
## 816 : param_names__.push_back(param_name_stream__.str());
## 817 : }
## 818 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 819 : param_name_stream__.str(std::string());
## 820 : param_name_stream__ << "ol_effect_m" << '.' << k_0__;
## 821 : param_names__.push_back(param_name_stream__.str());
## 822 : }
## 823 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 824 : param_name_stream__.str(std::string());
## 825 : param_name_stream__ << "recipe_effect_b" << '.' << k_0__;
## 826 : param_names__.push_back(param_name_stream__.str());
## 827 : }
## 828 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 829 : param_name_stream__.str(std::string());
## 830 : param_name_stream__ << "temp_effect_b" << '.' << k_0__;
## 831 : param_names__.push_back(param_name_stream__.str());
## 832 : }
## 833 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 834 : param_name_stream__.str(std::string());
## 835 : param_name_stream__ << "ol_effect_b" << '.' << k_0__;
## 836 : param_names__.push_back(param_name_stream__.str());
## 837 : }
## 838 : param_name_stream__.str(std::string());
## 839 : param_name_stream__ << "sigma";
## 840 : param_names__.push_back(param_name_stream__.str());
## 841 : param_name_stream__.str(std::string());
## 842 : param_name_stream__ << "sigma_b";
## 843 : param_names__.push_back(param_name_stream__.str());
## 844 :
## 845 : if (!include_gqs__ && !include_tparams__) return;
## 846 :
## 847 : if (include_tparams__) {
## 848 : for (int k_0__ = 1; k_0__ <= nrows; ++k_0__) {
## 849 : param_name_stream__.str(std::string());
## 850 : param_name_stream__ << "coli_hat" << '.' << k_0__;
## 851 : param_names__.push_back(param_name_stream__.str());
## 852 : }
## 853 : for (int k_0__ = 1; k_0__ <= nrows; ++k_0__) {
## 854 : param_name_stream__.str(std::string());
## 855 : param_name_stream__ << "cocci_hat" << '.' << k_0__;
## 856 : param_names__.push_back(param_name_stream__.str());
## 857 : }
## 858 : }
## 859 :
## 860 :
## 861 : if (!include_gqs__) return;
## 862 : }
## 863 :
## 864 :
## 865 : void unconstrained_param_names(std::vector<std::string>& param_names__,
## 866 : bool include_tparams__ = true,
## 867 : bool include_gqs__ = true) const {
## 868 : std::stringstream param_name_stream__;
## 869 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 870 : param_name_stream__.str(std::string());
## 871 : param_name_stream__ << "recipe_effect_m" << '.' << k_0__;
## 872 : param_names__.push_back(param_name_stream__.str());
## 873 : }
## 874 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 875 : param_name_stream__.str(std::string());
## 876 : param_name_stream__ << "temp_effect_m" << '.' << k_0__;
## 877 : param_names__.push_back(param_name_stream__.str());
## 878 : }
## 879 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 880 : param_name_stream__.str(std::string());
## 881 : param_name_stream__ << "ol_effect_m" << '.' << k_0__;
## 882 : param_names__.push_back(param_name_stream__.str());
## 883 : }
## 884 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 885 : param_name_stream__.str(std::string());
## 886 : param_name_stream__ << "recipe_effect_b" << '.' << k_0__;
## 887 : param_names__.push_back(param_name_stream__.str());
## 888 : }
## 889 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 890 : param_name_stream__.str(std::string());
## 891 : param_name_stream__ << "temp_effect_b" << '.' << k_0__;
## 892 : param_names__.push_back(param_name_stream__.str());
## 893 : }
## 894 : for (int k_0__ = 1; k_0__ <= 3; ++k_0__) {
## 895 : param_name_stream__.str(std::string());
## 896 : param_name_stream__ << "ol_effect_b" << '.' << k_0__;
## 897 : param_names__.push_back(param_name_stream__.str());
## 898 : }
## 899 : param_name_stream__.str(std::string());
## 900 : param_name_stream__ << "sigma";
## 901 : param_names__.push_back(param_name_stream__.str());
## 902 : param_name_stream__.str(std::string());
## 903 : param_name_stream__ << "sigma_b";
## 904 : param_names__.push_back(param_name_stream__.str());
## 905 :
## 906 : if (!include_gqs__ && !include_tparams__) return;
## 907 :
## 908 : if (include_tparams__) {
## 909 : for (int k_0__ = 1; k_0__ <= nrows; ++k_0__) {
## 910 : param_name_stream__.str(std::string());
## 911 : param_name_stream__ << "coli_hat" << '.' << k_0__;
## 912 : param_names__.push_back(param_name_stream__.str());
## 913 : }
## 914 : for (int k_0__ = 1; k_0__ <= nrows; ++k_0__) {
## 915 : param_name_stream__.str(std::string());
## 916 : param_name_stream__ << "cocci_hat" << '.' << k_0__;
## 917 : param_names__.push_back(param_name_stream__.str());
## 918 : }
## 919 : }
## 920 :
## 921 :
## 922 : if (!include_gqs__) return;
## 923 : }
## 924 :
## 925 : }; // model
## 926 :
## 927 : }
## 928 :
## 929 : typedef modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min stan_model;
## 930 :
## 931 : #include <rstan/rstaninc.hpp>
## 932 : /**
## 933 : * Define Rcpp Module to expose stan_fit's functions to R.
## 934 : */
## 935 : RCPP_MODULE(stan_fit4modeld8e35e346352_model_min_mod){
## 936 : Rcpp::class_<rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min,
## 937 : boost::random::ecuyer1988> >("stan_fit4modeld8e35e346352_model_min")
## 938 : // .constructor<Rcpp::List>()
## 939 : .constructor<SEXP, SEXP, SEXP>()
## 940 : // .constructor<SEXP, SEXP>()
## 941 : .method("call_sampler",
## 942 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::call_sampler)
## 943 : .method("param_names",
## 944 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::param_names)
## 945 : .method("param_names_oi",
## 946 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::param_names_oi)
## 947 : .method("param_fnames_oi",
## 948 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::param_fnames_oi)
## 949 : .method("param_dims",
## 950 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::param_dims)
## 951 : .method("param_dims_oi",
## 952 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::param_dims_oi)
## 953 : .method("update_param_oi",
## 954 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::update_param_oi)
## 955 : .method("param_oi_tidx",
## 956 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::param_oi_tidx)
## 957 : .method("grad_log_prob",
## 958 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::grad_log_prob)
## 959 : .method("log_prob",
## 960 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::log_prob)
## 961 : .method("unconstrain_pars",
## 962 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::unconstrain_pars)
## 963 : .method("constrain_pars",
## 964 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::constrain_pars)
## 965 : .method("num_pars_unconstrained",
## 966 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::num_pars_unconstrained)
## 967 : .method("unconstrained_param_names",
## 968 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::unconstrained_param_names)
## 969 : .method("constrained_param_names",
## 970 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::constrained_param_names)
## 971 : .method("standalone_gqs",
## 972 : &rstan::stan_fit<modeld8e35e346352_model_min_namespace::modeld8e35e346352_model_min, boost::random::ecuyer1988>::standalone_gqs)
## 973 : ;
## 974 : }
## 975 :
## 976 : // declarations
## 977 : extern "C" {
## 978 : SEXP filed8e3160ded43( ) ;
## 979 : }
## 980 :
## 981 : // definition
## 982 :
## 983 : SEXP filed8e3160ded43( ){
## 984 : return Rcpp::wrap("model_min");
## 985 : }
## 986 :
## 987 :
## Compilation argument:
## /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB filed8e3160ded43.cpp 2> filed8e3160ded43.cpp.err.txt
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:1:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Core:535:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:2:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/LU:47:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:3:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Cholesky:12:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Jacobi:29:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:3:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Cholesky:43:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/QR:17:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Householder:27:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:5:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/SVD:48:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:6:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Geometry:58:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:14:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Dense:7:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Eigenvalues:58:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:26:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/SparseCore:66:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:27:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/OrderingMethods:71:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:29:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/SparseCholesky:43:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:32:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/SparseQR:35:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:96:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/csr_extract_u.hpp:6:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/Sparse:33:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/IterativeLinearSolvers:46:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
## #pragma clang diagnostic pop
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:276:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_rng.hpp:5:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/gamma_distribution.hpp:25:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/exponential_distribution.hpp:27:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/int_float_pair.hpp:26:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead. [-W#pragma-messages]
## BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
## ^
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
## # define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
## ^
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
## # define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
## ^
## <scratch space>:235:2: note: expanded from here
## message("This header is deprecated. Use " "<boost/integer/integer_log2.hpp>" " instead.")
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core.hpp:44:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: unused function 'set_zero_all_adjoints' [-Wunused-function]
## static void set_zero_all_adjoints() {
## ^
## In file included from filed8e3160ded43.cpp:8:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/src/stan/model/model_header.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math.hpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/rev/mat.hpp:12:
## In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat.hpp:70:
## /Library/Frameworks/R.framework/Versions/3.5/Resources/library/StanHeaders/include/stan/math/prim/mat/fun/autocorrelation.hpp:18:8: warning: function 'fft_next_good_size' is not needed and will not be emitted [-Wunneeded-internal-declaration]
## size_t fft_next_good_size(size_t N) {
## ^
## 16 warnings generated.
##
## CHECKING DATA AND PREPROCESSING FOR MODEL 'model_min' NOW.
##
## COMPILING MODEL 'model_min' NOW.
##
## STARTING SAMPLER FOR MODEL 'model_min' NOW.
## Warning: There were 4 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
## http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
## Warning: Examine the pairs() plot to diagnose sampling problems
plot_pars <- names(fit)[!grepl("hat", names(fit))]
plot(fit, pars=plot_pars, plotfun = "trace", inc_warmup = F)
mcmc_rhat(rhat(fit)[plot_pars]) + yaxis_text(hjust = 0)
#ggplot(data.frame(x = c(-5, 5)), aes(x)) +
# stat_function(fun = dcauchy, n = 1e3, args = list(location = 0, scale = 1))
stan_dens(fit, pars=plot_pars[grepl("recipe", plot_pars)])
plot(fit, pars=plot_pars[grepl("recipe", plot_pars)])
## ci_level: 0.8 (80% intervals)
## outer_level: 0.95 (95% intervals)
stan_dens(fit, pars=plot_pars[grepl("temp", plot_pars)])
plot(fit, pars=plot_pars[grepl("temp", plot_pars)])
## ci_level: 0.8 (80% intervals)
## outer_level: 0.95 (95% intervals)
stan_dens(fit, pars=plot_pars[grepl("ol", plot_pars)])
plot(fit, pars=plot_pars[grepl("ol", plot_pars)])
## ci_level: 0.8 (80% intervals)
## outer_level: 0.95 (95% intervals)
plot(fit, pars=c("lp__"))
## ci_level: 0.8 (80% intervals)
## outer_level: 0.95 (95% intervals)
plot(fit, pars=c("sigma"))
## ci_level: 0.8 (80% intervals)
## outer_level: 0.95 (95% intervals)
#stan_model(fit)
(mle = optimizing(stan_model("./models/model_min.stan"), data=stan_data))
## $par
## recipe_effect_m[1] recipe_effect_m[2] recipe_effect_m[3]
## -0.06767946 -0.01880421 -0.04520354
## temp_effect_m[1] temp_effect_m[2] temp_effect_m[3]
## 0.08677723 0.09604484 -0.35941553
## ol_effect_m[1] ol_effect_m[2] ol_effect_m[3]
## -0.11183693 0.03651531 -0.06629225
## recipe_effect_b[1] recipe_effect_b[2] recipe_effect_b[3]
## -0.00770803 0.27782484 0.46710932
## temp_effect_b[1] temp_effect_b[2] temp_effect_b[3]
## 5.09900031 4.63578966 3.97356504
## ol_effect_b[1] ol_effect_b[2] ol_effect_b[3]
## 0.12205070 0.05701612 0.61687813
## sigma sigma_b coli_hat[1]
## 1.48220513 0.77431477 5.07438189
## coli_hat[2] coli_hat[3] coli_hat[4]
## 5.07438189 5.42500347 4.90361789
## coli_hat[5] coli_hat[6] coli_hat[7]
## 0.85431614 5.07438189 5.13117914
## coli_hat[8] coli_hat[9] coli_hat[10]
## 5.13117914 0.50765595 5.42500347
## coli_hat[11] coli_hat[12] coli_hat[13]
## 5.64882607 0.50765595 5.64882607
## coli_hat[14] coli_hat[15] coli_hat[16]
## 5.31514762 3.99888836 4.65690798
## coli_hat[17] coli_hat[18] coli_hat[19]
## 2.85113407 5.64882607 0.50765595
## coli_hat[20] coli_hat[21] coli_hat[22]
## 4.65690798 0.85431614 5.31514762
## coli_hat[23] coli_hat[24] coli_hat[25]
## 5.07438189 1.62241164 5.07438189
## coli_hat[26] coli_hat[27] coli_hat[28]
## 1.62241164 4.65690798 4.58273514
## coli_hat[29] coli_hat[30] coli_hat[31]
## 5.07438189 5.07438189 5.07438189
## coli_hat[32] coli_hat[33] coli_hat[34]
## 5.42500347 0.85431614 1.62241164
## coli_hat[35] coli_hat[36] coli_hat[37]
## 4.49971767 5.07438189 2.85113407
## coli_hat[38] coli_hat[39] coli_hat[40]
## 3.99888836 5.13117914 4.90361789
## coli_hat[41] coli_hat[42] coli_hat[43]
## 5.64882607 5.31514762 5.31514762
## coli_hat[44] coli_hat[45] coli_hat[46]
## 3.99888836 2.85113407 5.07438189
## coli_hat[47] coli_hat[48] coli_hat[49]
## 0.50765595 5.42500347 1.62241164
## coli_hat[50] coli_hat[51] coli_hat[52]
## 4.90361789 4.65690798 2.85113407
## coli_hat[53] coli_hat[54] coli_hat[55]
## 4.90361789 4.49971767 5.07438189
## coli_hat[56] coli_hat[57] coli_hat[58]
## 0.85431614 3.99888836 5.14830840
## coli_hat[59] coli_hat[60] coli_hat[61]
## 4.68509775 5.70817041 4.49971767
## coli_hat[62] coli_hat[63] coli_hat[64]
## 4.75013233 4.02287313 5.24495976
## coli_hat[65] coli_hat[66] coli_hat[67]
## 4.49971767 4.08790771 5.13117914
## coli_hat[68] coli_hat[69] coli_hat[70]
## 5.07438189 5.21334298 5.62902807
## coli_hat[71] coli_hat[72] coli_hat[73]
## 5.65316630 5.74730626 5.65316630
## coli_hat[74] coli_hat[75] coli_hat[76]
## 4.93187631 1.43310055 6.37423625
## coli_hat[77] coli_hat[78] coli_hat[79]
## 5.74730626 5.23569238 2.20119604
## coli_hat[80] coli_hat[81] coli_hat[82]
## 1.23306613 2.20119604 5.65316630
## coli_hat[83] coli_hat[84] coli_hat[85]
## 4.30840600 5.23569238 5.74730626
## coli_hat[86] coli_hat[87] coli_hat[88]
## 4.93187631 5.65316630 5.99370328
## coli_hat[89] coli_hat[90] coli_hat[91]
## 4.93187631 1.23306613 5.65316630
## coli_hat[92] coli_hat[93] coli_hat[94]
## 5.53049263 4.72429854 5.62902807
## coli_hat[95] coli_hat[96] coli_hat[97]
## 2.20119604 4.93187631 3.28329271
## coli_hat[98] coli_hat[99] coli_hat[100]
## 5.62902807 5.23569238 5.49887585
## coli_hat[101] coli_hat[102] coli_hat[103]
## 6.37423625 1.23306613 3.28329271
## coli_hat[104] coli_hat[105] coli_hat[106]
## 6.37423625 4.97063062 5.65316630
## coli_hat[107] coli_hat[108] coli_hat[109]
## 6.00378788 4.72429854 6.00378788
## coli_hat[110] coli_hat[111] coli_hat[112]
## 5.56333778 5.74730626 3.28329271
## coli_hat[113] coli_hat[114] coli_hat[115]
## 6.37423625 5.62902807 1.43310055
## coli_hat[116] coli_hat[117] coli_hat[118]
## 1.23306613 3.28329271 2.20119604
## coli_hat[119] coli_hat[120] coli_hat[121]
## 6.00378788 5.43384127 4.72429854
## coli_hat[122] coli_hat[123] coli_hat[124]
## 4.37344058 5.56333778 4.72429854
## coli_hat[125] coli_hat[126] coli_hat[127]
## 5.65316630 1.43310055 5.03566520
## coli_hat[128] coli_hat[129] coli_hat[130]
## 5.65316630 6.00378788 5.56333778
## coli_hat[131] coli_hat[132] coli_hat[133]
## 5.65316630 5.65316630 5.56333778
## coli_hat[134] coli_hat[135] coli_hat[136]
## 5.65316630 5.23569238 5.65316630
## coli_hat[137] coli_hat[138] coli_hat[139]
## 1.43310055 4.86826801 2.23208454
## coli_hat[140] coli_hat[141] coli_hat[142]
## 3.39337920 1.18475663 1.46398904
## coli_hat[143] coli_hat[144] coli_hat[145]
## 5.68405479 5.68405479 5.67342426
## coli_hat[146] coli_hat[147] coli_hat[148]
## 5.58071857 4.67598904 5.68405479
## coli_hat[149] coli_hat[150] coli_hat[151]
## 5.68405479 1.18475663 6.32592675
## coli_hat[152] coli_hat[153] coli_hat[154]
## 5.04196280 1.46398904 5.85739275
## coli_hat[155] coli_hat[156] coli_hat[157]
## 3.39337920 5.68405479 4.67598904
## coli_hat[158] coli_hat[159] coli_hat[160]
## 1.46398904 5.68405479 5.26658088
## coli_hat[161] coli_hat[162] coli_hat[163]
## 5.04196280 6.03467638 5.58071857
## coli_hat[164] coli_hat[165] coli_hat[166]
## 3.39337920 5.68405479 6.32592675
## coli_hat[167] coli_hat[168] coli_hat[169]
## 6.03467638 5.85739275 4.67598904
## coli_hat[170] coli_hat[171] coli_hat[172]
## 5.26658088 5.68405479 6.32592675
## coli_hat[173] coli_hat[174] coli_hat[175]
## 6.03467638 5.67342426 2.23208454
## coli_hat[176] coli_hat[177] coli_hat[178]
## 6.03467638 5.68405479 5.04196280
## coli_hat[179] coli_hat[180] coli_hat[181]
## 1.18475663 2.23208454 5.67342426
## coli_hat[182] coli_hat[183] coli_hat[184]
## 6.32592675 4.67598904 5.26658088
## coli_hat[185] coli_hat[186] coli_hat[187]
## 5.85739275 1.18475663 5.22494968
## coli_hat[188] coli_hat[189] coli_hat[190]
## 5.15991510 5.71977711 5.67342426
## coli_hat[191] coli_hat[192] coli_hat[193]
## 2.23208454 5.58071857 1.46398904
## coli_hat[194] coli_hat[195] coli_hat[196]
## 5.58071857 5.04196280 5.68816033
## coli_hat[197] coli_hat[198] coli_hat[199]
## 5.62312574 6.18298776 5.85739275
## coli_hat[200] coli_hat[201] coli_hat[202]
## 5.26658088 3.39337920 5.68405479
## coli_hat[203] coli_hat[204] coli_hat[205]
## 5.68405479 5.68405479 4.56272506
## coli_hat[206] coli_hat[207] cocci_hat[1]
## 4.49769048 5.05755249 5.07438189
## cocci_hat[2] cocci_hat[3] cocci_hat[4]
## 5.07438189 5.42500347 4.90361789
## cocci_hat[5] cocci_hat[6] cocci_hat[7]
## 0.85431614 5.07438189 5.13117914
## cocci_hat[8] cocci_hat[9] cocci_hat[10]
## 5.13117914 0.50765595 5.42500347
## cocci_hat[11] cocci_hat[12] cocci_hat[13]
## 5.64882607 0.50765595 5.64882607
## cocci_hat[14] cocci_hat[15] cocci_hat[16]
## 5.31514762 3.99888836 4.65690798
## cocci_hat[17] cocci_hat[18] cocci_hat[19]
## 2.85113407 5.64882607 0.50765595
## cocci_hat[20] cocci_hat[21] cocci_hat[22]
## 4.65690798 0.85431614 5.31514762
## cocci_hat[23] cocci_hat[24] cocci_hat[25]
## 5.07438189 1.62241164 5.07438189
## cocci_hat[26] cocci_hat[27] cocci_hat[28]
## 1.62241164 4.65690798 4.58273514
## cocci_hat[29] cocci_hat[30] cocci_hat[31]
## 5.07438189 5.07438189 5.07438189
## cocci_hat[32] cocci_hat[33] cocci_hat[34]
## 5.42500347 0.85431614 1.62241164
## cocci_hat[35] cocci_hat[36] cocci_hat[37]
## 4.49971767 5.07438189 2.85113407
## cocci_hat[38] cocci_hat[39] cocci_hat[40]
## 3.99888836 5.13117914 4.90361789
## cocci_hat[41] cocci_hat[42] cocci_hat[43]
## 5.64882607 5.31514762 5.31514762
## cocci_hat[44] cocci_hat[45] cocci_hat[46]
## 3.99888836 2.85113407 5.07438189
## cocci_hat[47] cocci_hat[48] cocci_hat[49]
## 0.50765595 5.42500347 1.62241164
## cocci_hat[50] cocci_hat[51] cocci_hat[52]
## 4.90361789 4.65690798 2.85113407
## cocci_hat[53] cocci_hat[54] cocci_hat[55]
## 4.90361789 4.49971767 5.07438189
## cocci_hat[56] cocci_hat[57] cocci_hat[58]
## 0.85431614 3.99888836 5.14830840
## cocci_hat[59] cocci_hat[60] cocci_hat[61]
## 4.68509775 5.70817041 4.49971767
## cocci_hat[62] cocci_hat[63] cocci_hat[64]
## 4.75013233 4.02287313 5.24495976
## cocci_hat[65] cocci_hat[66] cocci_hat[67]
## 4.49971767 4.08790771 5.13117914
## cocci_hat[68] cocci_hat[69] cocci_hat[70]
## 5.07438189 5.21334298 5.62902807
## cocci_hat[71] cocci_hat[72] cocci_hat[73]
## 5.65316630 5.74730626 5.65316630
## cocci_hat[74] cocci_hat[75] cocci_hat[76]
## 4.93187631 1.43310055 6.37423625
## cocci_hat[77] cocci_hat[78] cocci_hat[79]
## 5.74730626 5.23569238 2.20119604
## cocci_hat[80] cocci_hat[81] cocci_hat[82]
## 1.23306613 2.20119604 5.65316630
## cocci_hat[83] cocci_hat[84] cocci_hat[85]
## 4.30840600 5.23569238 5.74730626
## cocci_hat[86] cocci_hat[87] cocci_hat[88]
## 4.93187631 5.65316630 5.99370328
## cocci_hat[89] cocci_hat[90] cocci_hat[91]
## 4.93187631 1.23306613 5.65316630
## cocci_hat[92] cocci_hat[93] cocci_hat[94]
## 5.53049263 4.72429854 5.62902807
## cocci_hat[95] cocci_hat[96] cocci_hat[97]
## 2.20119604 4.93187631 3.28329271
## cocci_hat[98] cocci_hat[99] cocci_hat[100]
## 5.62902807 5.23569238 5.49887585
## cocci_hat[101] cocci_hat[102] cocci_hat[103]
## 6.37423625 1.23306613 3.28329271
## cocci_hat[104] cocci_hat[105] cocci_hat[106]
## 6.37423625 4.97063062 5.65316630
## cocci_hat[107] cocci_hat[108] cocci_hat[109]
## 6.00378788 4.72429854 6.00378788
## cocci_hat[110] cocci_hat[111] cocci_hat[112]
## 5.56333778 5.74730626 3.28329271
## cocci_hat[113] cocci_hat[114] cocci_hat[115]
## 6.37423625 5.62902807 1.43310055
## cocci_hat[116] cocci_hat[117] cocci_hat[118]
## 1.23306613 3.28329271 2.20119604
## cocci_hat[119] cocci_hat[120] cocci_hat[121]
## 6.00378788 5.43384127 4.72429854
## cocci_hat[122] cocci_hat[123] cocci_hat[124]
## 4.37344058 5.56333778 4.72429854
## cocci_hat[125] cocci_hat[126] cocci_hat[127]
## 5.65316630 1.43310055 5.03566520
## cocci_hat[128] cocci_hat[129] cocci_hat[130]
## 5.65316630 6.00378788 5.56333778
## cocci_hat[131] cocci_hat[132] cocci_hat[133]
## 5.65316630 5.65316630 5.56333778
## cocci_hat[134] cocci_hat[135] cocci_hat[136]
## 5.65316630 5.23569238 5.65316630
## cocci_hat[137] cocci_hat[138] cocci_hat[139]
## 1.43310055 4.86826801 2.23208454
## cocci_hat[140] cocci_hat[141] cocci_hat[142]
## 3.39337920 1.18475663 1.46398904
## cocci_hat[143] cocci_hat[144] cocci_hat[145]
## 5.68405479 5.68405479 5.67342426
## cocci_hat[146] cocci_hat[147] cocci_hat[148]
## 5.58071857 4.67598904 5.68405479
## cocci_hat[149] cocci_hat[150] cocci_hat[151]
## 5.68405479 1.18475663 6.32592675
## cocci_hat[152] cocci_hat[153] cocci_hat[154]
## 5.04196280 1.46398904 5.85739275
## cocci_hat[155] cocci_hat[156] cocci_hat[157]
## 3.39337920 5.68405479 4.67598904
## cocci_hat[158] cocci_hat[159] cocci_hat[160]
## 1.46398904 5.68405479 5.26658088
## cocci_hat[161] cocci_hat[162] cocci_hat[163]
## 5.04196280 6.03467638 5.58071857
## cocci_hat[164] cocci_hat[165] cocci_hat[166]
## 3.39337920 5.68405479 6.32592675
## cocci_hat[167] cocci_hat[168] cocci_hat[169]
## 6.03467638 5.85739275 4.67598904
## cocci_hat[170] cocci_hat[171] cocci_hat[172]
## 5.26658088 5.68405479 6.32592675
## cocci_hat[173] cocci_hat[174] cocci_hat[175]
## 6.03467638 5.67342426 2.23208454
## cocci_hat[176] cocci_hat[177] cocci_hat[178]
## 6.03467638 5.68405479 5.04196280
## cocci_hat[179] cocci_hat[180] cocci_hat[181]
## 1.18475663 2.23208454 5.67342426
## cocci_hat[182] cocci_hat[183] cocci_hat[184]
## 6.32592675 4.67598904 5.26658088
## cocci_hat[185] cocci_hat[186] cocci_hat[187]
## 5.85739275 1.18475663 5.22494968
## cocci_hat[188] cocci_hat[189] cocci_hat[190]
## 5.15991510 5.71977711 5.67342426
## cocci_hat[191] cocci_hat[192] cocci_hat[193]
## 2.23208454 5.58071857 1.46398904
## cocci_hat[194] cocci_hat[195] cocci_hat[196]
## 5.58071857 5.04196280 5.68816033
## cocci_hat[197] cocci_hat[198] cocci_hat[199]
## 5.62312574 6.18298776 5.85739275
## cocci_hat[200] cocci_hat[201] cocci_hat[202]
## 5.26658088 3.39337920 5.68405479
## cocci_hat[203] cocci_hat[204] cocci_hat[205]
## 5.68405479 5.68405479 4.56272506
## cocci_hat[206] cocci_hat[207]
## 4.49769048 5.05755249
##
## $value
## [1] -248.229
##
## $return_code
## [1] 0
